Vitória S. Reis, Luciana Guimarães, Clebio S. Nascimento Jr.
{"title":"A computational study on the enantioselective separation of cyhalothrin enantiomers by β-cyclodextrins","authors":"Vitória S. Reis, Luciana Guimarães, Clebio S. Nascimento Jr.","doi":"10.1007/s00894-025-06469-7","DOIUrl":"10.1007/s00894-025-06469-7","url":null,"abstract":"<div><h3>Context</h3><p>This computational study investigates the enantioselective separation of λ-cyhalothrin (CLT) enantiomers, ( +)-[S]-CLT and ( −)-[R]-CLT, using native β-cyclodextrin (β-CD) and its sulfated derivative (S-β-CD) as chiral selectors. Our calculations, employing B97D/6-31G(d,p)//PM3 and B97X-D3/6-31G(d,p)//GFN2-xTB methodologies, consistently demonstrate that the ( −)-[R]-CLT enantiomer forms more stable inclusion complexes with both selectors, predicting a longer migration time compared to ( +)-[S]-CLT. This enhanced stability is primarily due to favorable hydrophobic interactions, with additional hydrogen bonding contributing in the case of S-β-CD. S-β-CD exhibited superior separation efficiency, as evidenced by higher ΔΔ<i>G</i> values, likely due to structural modifications induced by sulfate groups that optimize steric fitting and van der Waals interactions within the cyclodextrin cavity. These findings highlight the potential of S-β-CD for efficient enantiomeric separation of CLT and underscore the utility of computational chemistry in understanding chiral recognition mechanisms.</p><h3>Methods</h3><p>Two distinct theoretical methodologies, B97D/6-31G(d,p)//PM3 and ωB97X-D3/6-31G(d,p)//GFN2-xTB, were employed to elucidate the structural and energetic properties of these diastereomeric complexes. The calculations were performed on Gaussian 09 and ORCA 5.0 software packages.\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144810951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Theoretical analysis of atomic electronegativity effects on excited state behaviors for HBT-PhCz derivatives","authors":"Le Zhang, Jiahe Chen, Rivaille Liu, Haohua Zhang, Dongxiao Li, Jinfeng Zhao","doi":"10.1007/s00894-025-06465-x","DOIUrl":"10.1007/s00894-025-06465-x","url":null,"abstract":"<div><h3>Context</h3><p>The excited-state intramolecular proton transfer (ESIPT) reaction of 9-phenyl-9H-carbazole substituted 2-hydroxyphenyl benzothiazole (HBT-PhCz) derivatives is studied based on TDDFT/B3LYP/TZVP theoretical level. To provide direct information on the effect of atomic electronegativity on the ESIPT reactions, the geometric parameters, infrared (IR) vibrational spectra, core-valence bifurcation (CVB) index coupling with predicting the hydrogen bonding energy (E<sub>HB</sub>), vertical excitation behaviors, frontier molecular orbitals (MOs), and potential energy curves have been calculated for chalcogen-substituted HBT-PhCz derivatives (HBT-PhCz-O, HBT-PhCz-S, and HBT-PhCz-Se). The charge recombination caused by photoexcitation and energy gap between HOMO and LUMO orbitals further reveal the ESIPT trend. Potential energy curves of the three molecules under consideration are examined, with the conclusion being drawn that the ESIPT behaviors could be regulated by chalcogen element substitutions. In brief, we propose the ESIPT mechanism and spectral behavior of atomic electronegativity regulation for HBT-PhCz derivatives.</p><h3>Methods</h3><p>All molecular structures have been optimized using DFT and TDDFT methods with D3-B3LYP and TZVP levels by Gaussian 16 software. Vertical excitation simulations are based on TDDFT method with analyzing charge redistribution behaviors. Using the Multiwfn 3.8 software, the core-valence bifurcation (CVB) indexes are performed. Further, the potential energy surfaces have been constructed, based on which the transition state (TS) configurations are searched at the same theoretical level.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144810953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The structural view of the protein PGD-219aa encoded by the circular RNA CircPGD","authors":"Jit Mondal, Sima Biswas, Sreekanya Roy, Anirban Nandy, Dipanjan Guha, Angshuman Bagchi","doi":"10.1007/s00894-025-06454-0","DOIUrl":"10.1007/s00894-025-06454-0","url":null,"abstract":"<p>Circular RNAs (circRNAs), belonging to the class of non-coding RNA molecules, have emerged as one of the key regulators of gene expression. Some of the circRNAs have proven protein-coding potentials, and their gene products play significant roles in various physiological and pathological processes. One such protein is PGD-219aa, which is derived from the circRNA named CircPGD. The protein has been shown to regulate the SMAD3 and YAP signalling pathways in gastric cancer. However, only the amino acid sequence of the protein is available to date without any reports on its structure–function relationships. Therefore, we used computational methods to characterise the protein and decipher its functional roles. Furthermore, we performed pathway analyses to shed light on the biochemical avenues where the protein might have a significant presence. From our analyses, we could point towards the importance of a key amino acid residue, Ser177, which might have fundamental functional roles. Future studies might involve targeting this particular amino acid to delineate its functional characteristics. Subsequently, we could propose the association of the protein not only to gastric cancer but also with other diseases as well. Through this work, we tried to analyse the plausible details of the functional roles of the protein. Our work may help in future drug development endeavours to combat the spread of gastric cancer tumours.</p><p>Circular RNAs (circRNAs), belonging to the class of non-coding RNA molecules, have emerged as one of the key regulators of gene expression. Some of the circRNAs have proven protein-coding potentials, and their gene products play significant roles in various physiological and pathological processes. One such protein is PGD-219aa, which is derived from the circRNA named CircPGD. The protein has been shown to regulate the SMAD3 and YAP signalling pathways in gastric cancer. However, only the amino acid sequence of the protein is available to date without any reports on its structure-function relationships. From our analyses, we could point towards the importance of a key amino acid residue, Ser177, which might have fundamental functional roles. Future studies might involve targeting this particular amino acid to delineate its functional characteristics. Subsequently, we could propose the association of the protein not only to gastric cancer but also with other diseases as well. Through this work, we tried to analyse the plausible details of the functional roles of the protein. Our work may help in future drug development endeavours to combat the spread of gastric cancer tumours.</p><p>Therefore, we used computational methods to characterise the protein and decipher its functional roles. Furthermore, we performed pathway analyses to shed light on the biochemical avenues where the protein might have a significant presence.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hicham Mahdjoub–Araibi, Mourad Zouaoui–Rabah, Madani Hedidi, Abdelkader M. Elhorri, Assia Laib, Mohammed Zenati
{"title":"DFT and TD–DFT study of push–pull molecules with extended conjugated bridges: theoretical insight into organometallic rings for the enhanced Nonlinear Optical (NLO) properties","authors":"Hicham Mahdjoub–Araibi, Mourad Zouaoui–Rabah, Madani Hedidi, Abdelkader M. Elhorri, Assia Laib, Mohammed Zenati","doi":"10.1007/s00894-025-06445-1","DOIUrl":"10.1007/s00894-025-06445-1","url":null,"abstract":"<div><h3>Context</h3><p>This work presents a theoretical investigation of nine push–pull molecules featuring conjugated bridges composed of three distinct organometallic rings: Titanol, Chromol, Ferrol, Nickelol, and Zinkol. These bridges are connected at their ends to acceptor (NO₂) and donor (N(CH₃)₂) groups positioned on the α-sites of the aforementioned rings. In systems incorporating cyclic groups, it was found that placing Titanol and Nickelol rings between two Zinkol units enhances the nonlinear optical (NLO) response. A similar enhancement is observed when Chromol and Ferrol rings are positioned at the termini of the Zinkol units. Frontier orbital analysis reveals that the Zinkol rings exhibit electron-accepting characteristics, whereas the other rings act as electron donors. The two molecular systems conform to the architectures D–A–D–A–A (Titanol–Nichelol–Zinkol) and D–D–A–A–A (Chromol–Ferrol–Zinkol), respectively. Computed static β_tot values range from 142.71 to 512.07 × 10<sup>–30</sup> esu, while static |γav| values fall within 1.88 to 245.05 × 10⁻<sup>35</sup> esu. The study also includes an analysis of dynamic <span>({beta }_{||}^{lambda }(-2omega ;omega ,omega ))</span> values, which lie between 2478.43 and 1,036,410.00 × 10<sup>–30</sup> esu, and dynamic <span>({gamma }_{||}^{lambda }(-2omega ;omega ,omega ,0))</span> values ranging from 26,017.87 to 193,013,000 × 10⁻<sup>35</sup> esu. Nonlinear refractive indices (n₂) were also evaluated, with values spanning from 5.11 × 10⁻<sup>15</sup> cm<sup>2</sup>·W⁻<sup>1</sup> to 2.91 × 10⁻<sup>1</sup>⁰ cm<sup>2</sup>·W⁻<sup>1</sup>. Additionally, most of the investigated molecules exhibit absorption within the 450–900 nm range, both in vacuum and in various solvents.</p><h3>Method</h3><p>All calculations were performed using Gaussian 16 program. The methods used are DFT and TD–DFT.Several functionals were treated: CAM–B3LYP, LC–ωPBE, LC–BLYP, M11, ωB97X, M08HX, M062X, MN12SX, MN15, M06HF.Several basis–sets was studied:6–31G(d,p), 6–31 + + G(d,p), cc–pVDZ, AUG–cc–pVDZ, 6–311G(d,p), 6–311 + + G(d,p), cc–pVTZ, AUG–cc–pVTZ and LanL2DZ. Implicit Solvation Model used are CPCM and SMD. Finally, NBO method is used also.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Haojie Dang, Wenchao Tian, Yongkun Wang, Si Chen, Hanyang Xu
{"title":"Atomic-scale theoretical investigation into the role of metal passivation layers in lowering Cu-Cu bonding temperature","authors":"Haojie Dang, Wenchao Tian, Yongkun Wang, Si Chen, Hanyang Xu","doi":"10.1007/s00894-025-06446-0","DOIUrl":"10.1007/s00894-025-06446-0","url":null,"abstract":"<div><h3>Context</h3><p>Low-temperature Cu-Cu bonding is critical for 3D integration. Metal passivation layers promote this bonding, but their atomic mechanisms are not fully understood. Here, molecular dynamics simulations investigate how these layers enhance atomic diffusion and reduce bonding temperature. Results show that increasing temperature and time accelerate diffusion, temperature dominates diffusion via its exponential effect on the diffusion coefficient, while time linearly influences only the diffusion distance. The choice of metal passivation layer significantly influences the process. Titanium (Ti) most effectively facilitates diffusion. Initially, diffusion in the passivation layer resembles bulk metal interdiffusion, but over time, the formation of numerous and deeper grain boundaries within the passivation layer occurs, marking a shift toward low-energy grain boundary diffusion. It promotes low-temperature Cu-Cu bonding. Polycrystalline gold, with its initial grain boundaries, further accelerates diffusion and lowers the activation energy for bonding. Therefore, grain refinement is identified as an effective means of enhancing atomic diffusion and bonding quality. This work provides theoretical insights into lowering the temperature of Cu-Cu bonding and offers scientific foundations for optimizing bonding processes.</p><h3>Methods</h3><p>Molecular dynamics (MD) simulations using the LAMMPS package were conducted to study Cu-Cu bonding with various metal passivation layers (Ag, Au, Ti, polycrystalline Au). The Cu-passivation layer-Cu model was constructed, with atomic interactions described by the MEAM potential. Diffusion behavior was simulated under the NVT ensemble at target temperatures for 300 ps. The bonding interface evolution was visualized using OVITO, and diffusion coefficients and activation energies were derived from the mean square displacement (MSD), enabling inference of the passivation layer’s role in Cu-Cu bonding.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144787939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Corona VRus Coaster: the virtual reality roller coaster of the proteins of SARS-CoV-2","authors":"Alejandro Seco-González, César Porto, Ángel Piñeiro, Rebeca Garcia-Fandino","doi":"10.1007/s00894-025-06455-z","DOIUrl":"10.1007/s00894-025-06455-z","url":null,"abstract":"<div><h3>Context</h3><p>The COVID-19 pandemic, caused by SARS-CoV-2, has driven significant research into the virus’ structural components to elucidate its infection mechanisms and advance therapeutic strategies. However, the intricate architecture of viral proteins presents challenges for researchers and students in structural biology. To address this, we developed Corona VRus Coaster, a virtual reality (VR) application designed to facilitate molecular visualization. This tool enables immersive exploration of over 2000 viral proteins, including key structures such as the spike protein, nucleocapsid protein, main protease, and RNA-dependent RNA polymerase. Users can “ride” along the molecular backbones of these proteins, offering a distinctive way to explore their three-dimensional organization. Hand-tracking technology provides an intuitive interface for real-time interaction, while multiple visualization and navigation modes enhance the exploration experience. This application offers a novel and engaging approach to structural biology, supporting both research and education by making molecular structures more accessible and interactive. Corona VRus Coaster is available for download at http://mduse.com/coronavruscoaster.</p><h3>Methods</h3><p>Corona VRus Coaster was developed using Unity3D and integrates molecular visualization frameworks such as the Molecular Rift toolkit for VR rendering. Protein structures were sourced from the Protein Data Bank (PDB) and converted into VR-compatible formats using Open Babel and PyMOL. The application employs hand-tracking technology via the Meta Interaction SDK to facilitate direct manipulation of molecular structures. The visualization modes incorporate different molecular representations, including ribbon, surface, and space-filling models, rendered using GPU-accelerated shaders. Navigation is enabled through VR motion controllers and gaze-based selection mechanisms. The modular software architecture allows seamless integration of newly resolved protein structures, ensuring flexibility for future molecular visualization applications.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12328519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144787940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nabela Audryna Amalia Insani, Nurwarrohman Andre Sasongko, Suci Zulaikha Hildayani, Dwi Hudiyanti, Khairul Anam, Daniel Sethio, Vivitri Dewi Prasasty, Parsaoran Siahaan
{"title":"Influence of carboxymethyl chitosan chain length on its interaction with vitamin C and curcumin: molecular docking and molecular dynamic approach","authors":"Nabela Audryna Amalia Insani, Nurwarrohman Andre Sasongko, Suci Zulaikha Hildayani, Dwi Hudiyanti, Khairul Anam, Daniel Sethio, Vivitri Dewi Prasasty, Parsaoran Siahaan","doi":"10.1007/s00894-025-06458-w","DOIUrl":"10.1007/s00894-025-06458-w","url":null,"abstract":"<div><h3>Context</h3><p>The molecular understanding of the interaction between carboxymethyl chitosan (CMCs) with the encapsulated drug (vitamin C and curcumin) has not been clearly understood yet. This study seeks to ascertain how the polymer length affects the molecular weight of CMCs as a matrix by using molecular dynamics and molecular docking. We have used pentamer (N-CMCs-5), decamer (N-CMCs-10), and pentadecamer(N-CMCs-15). Molecular docking and dynamic simulations showcase diverse interaction strengths, revealing medium-to-weak hydrogen bonds and hydrophobic interactions within the N-CMCs…vitamin C and N-CMCs…curcumin complexes. Notably, N-CMCs-5…vitamin C (− 17.23 kJ/mol) and N-CMCs-10…curcumin (− 19.74 kJ/mol) exhibit the most robust interactions. RMSD analysis underscores the superior stability of N-CMCs-5…vitamin C (6.70 ± 1.68) and N-CMCs-5…curcumin (8.62 ± 2.47), particularly in comparison to other complexes. Stability in the solid phase relies on medium hydrogen bonds, while solution-phase stability hinges on hydrophobic interactions. Intriguingly, distance analysis highlights the exceptional stability of N-CMCs-5…vitamin C and N-CMCs-15…curcumin, maintaining distances below 3.2 Å during a 100 ns simulation, indicating robust complex stability. The binding constant of N-CMCs-5…vitamin C and N-CMCs-15…curcumin respectively 0.96 mM and 0.39 mM. The findings emphasize the influential role of longer polymer conformations in regulating drug release. Sequential docking studies revealed that curcumin has the capacity to stabilize the complexes, whereas vitamin C tends to destabilize them.</p><h3>Methods</h3><p>The molecular docking method was carried out in grid boxes measuring 10 × 10 × 10 Å using the YASARA software. Docking was performed at a temperature of 298.15 K using the VINA algorithm. Molecular docking generates conformation of the receptor-ligand complex, binding site between ligand and receptor, and the energy of complex interactions. Molecular dynamics simulations have been simulated using the same software but utilizing the AMBER14 force field for 100 ns at 298.15 K through many steps of solvation, neutralization, minimization, equilibrium, production, and trajectory analysis. Molecular dynamics are simulated by solvating in a 10 × 10 × 10 Å periodic boundary box. The solvation procedure employs a TIP3P (Transferable Intermolecular Potential 3-Point) water solvent system with a pH of 7.4 and a density of 0.997 g/L.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144787941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Douglas Sifuna, Solomon Omwoma, Silas Lagat, Felix Okello, Favour A. Nelson, Anthony Pembere
{"title":"Retraction Note: Theory guided engineering of zeolite adsorbents for acaricide residue adsorption from the environment","authors":"Douglas Sifuna, Solomon Omwoma, Silas Lagat, Felix Okello, Favour A. Nelson, Anthony Pembere","doi":"10.1007/s00894-025-06461-1","DOIUrl":"10.1007/s00894-025-06461-1","url":null,"abstract":"","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144787942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohnish Mohnish, Vijayalakshmi Ramavath, Vikas D. Ghule, Radhakrishnan Sarangapani
{"title":"Computation of 1H NMR chemical shifts: structural assessment of energetic materials","authors":"Mohnish Mohnish, Vijayalakshmi Ramavath, Vikas D. Ghule, Radhakrishnan Sarangapani","doi":"10.1007/s00894-025-06448-y","DOIUrl":"10.1007/s00894-025-06448-y","url":null,"abstract":"<div><h3>Context</h3><p>Nuclear magnetic resonance (NMR) spectroscopy is a highly valuable tool that is extensively employed for the structure elucidation of organic compounds and in various domains of chemistry. The density functional theory (DFT) and gauge-independent atomic orbital (GIAO) calculation strategy was established to predict reliable NMR chemical shifts with low computational expense and assist in resolving ambiguities in complex structure assignments. Here, we present the DFT-GIAO NMR chemical shift prediction method employed for the first time on a variety of energetic materials. We have predicted <sup>1</sup>H NMR shifts using computationally inexpensive single-point calculations for 48 energetic compounds comprising aliphatic, aromatic and heterocyclic backbones with various explosophoric functionalities. In DFT optimization and GIAO NMR computations at the B3LYP/6-311G+(2d,p) level, we predicted the <sup>1</sup>H chemical shifts for various energetic compounds and validated them with corresponding experimentally measured NMR spectra. The mean absolute deviation in predicted <sup>1</sup>H NMR shifts in CH protons ranges from 0.01 to 2.15 ppm. We illustrate the application of B3LYP/6-311G+(2d,p) method to assign the stereochemistry or highly deshielded protons due to electronegative explosophoric groups in energetic compounds with reasonable accuracy. This study also establishes the structure-chemical shift relationships of energetic materials. We believe that the reliable structural assignments provided by the DFT-GIAO method offer a user-friendly yet underutilized tool for structural validation and assignment of ambiguous and complex energetic molecular structures.</p><h3>Methods</h3><p>The optimization and proton chemical shift prediction for all selected energetic compounds were carried out at the B3LYP/6-311G+(2d,p) level of theory, utilizing Gaussian 09 software package.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structure and properties of 1,3,5-triazine and 1,2,4-triazole linked energetic derivatives with varied energetic functional groups","authors":"Zikai Gao, Zhihui Gu, Mengjie Bao, Peng Ma","doi":"10.1007/s00894-025-06462-0","DOIUrl":"10.1007/s00894-025-06462-0","url":null,"abstract":"<div><h3>Context</h3><p>A series of 49 derivatives, designed as the A series, were theoretically modeled by connecting 1,3,5-triazine and 1,2,4-triazole moieties via a direct C–N linkage. The properties of these compounds, incorporating various substituent combinations, were systematically investigated. Computational analysis revealed that nitro, nitrate ester, and nitramino groups significantly enhance the oxygen balance of the designed energetic molecules. Furthermore, the azide and cyano groups were found to contribute substantially to the heat of formation. Intramolecular interaction studies indicated that nitramino facilitates hydrogen bond formation. Screening identified compound A6-6 as exhibiting the optimal detonation characteristics, with a specific energy (<i>Q</i>) of 6.02 kJ/g, detonation velocity (<i>D</i>) of 8.64 km/s, and detonation pressure (<i>P</i>) of 34.24 GPa. Additionally, A6-6 exhibits a density (1.909 g/cm<sup>3</sup>) surpassing HMX and superior oxygen balance.</p><h3>Method</h3><p>Structural optimizations of all 49 derivatives were performed using the DFT-D3-B3LYP functional with the 6-311G**(d,p) basis set in Gaussian 16, followed by single-point energy calculations employing the M06-2X-D3/def2-TZVPP basis set. Wavefunction analysis was conducted using Multiwfn 3.8 package.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}